Mass Effect: Confederation
by Airaviper
Summary: The war is over. The Reapers have been destroyed. The races of the galaxy survived the greatest threat ever known. Now, they have to pick up the pieces. With Cerberus on the rise again and old grudges resurfacing, can a fledgling Systems Alliance unite a broken galaxy? *Will be updated every week if possible*
1. Introduction

Mass Effect: Confederation

Onboard the SSV United Earth, Admiral Steve Hackett gazed out the bridge windows into the empty void of FTL space. He didn't know what to expect. Just hours earlier, the crucible fired, and the entirety of Sword Fleet jumped away to a nearby system. Now they were FTL jumping back to Earth, and he was worried. Sure, the red shockwave of energy that the crucible unleashed didn't effect the ships of Sword Fleet, but they were light years away from the epicenter. "Who knows what the blast could have done to Earth? " he thought. "Hell who even knows if the blast killed the Reapers?"

An ensign spoke up on the bridge. "Sir, we have almost reached the Sol System, ETA: 10 seconds."

The admiral merely gave the ensign a nod as he prepared himself for whatever happened to Earth.

"Five, four, three, two, one!" Right as the Ensign finished counting down, the ship shook as it decelerated out of FTL. All around the United Earth, the surviving vessels of sword fleet appeared, all forming up on the flagship's wing.

"Set course for Earth ensign. Full sub light speed." Hackett ordered. The combined fleet made its way past the various other planets of Sol until they finally came in view of Earth.

"Shields up, arm all weapons. We don't know if the Reapers were destroyed or not. Take us in helmsman." Hackett said, as the remaining vessels of Sword Fleet pulled up to Earth.

"Sir, we are being hailed by the HSV Endurance." A bridge officer said.

"On screen." Hackett ordered.

"Admiral! We have a confirmed Reaper dead. We are scanning it and there are no energy readings coming from it whatsoever."

More hails came in from ships across the fleet. All of them saying the same thing: The Reapers were dead. The Crucible did its job. Hackett was overjoyed, but he didn't want to start celebrating yet.

Just then, the mangled remains of the Citadel came into view. The entire center had been destroyed, with the various arms splintered apart, stuck in Earth orbit, The entire bridge was silent with horror as it came into view. Who knew how many people were still onboard it whenever it blew. And what about Shepard?

"Ensign, open a hailing frequency. Just see if anybody answers, Citadel or Earth, I don't care." Hackett barked.

Nothing but static.

Hackett sighed. Sure, they may have saved Earth, but who even knows if it's habitable anymore? What if the Crucible destroyed Hammer Team as well as the Reapers? So much uncertainty.

There was suddenly a small break in the static.

"This is Major Coats of Hammer Team, is anybody there? I Repeat, this is Major Coats of Hammer team to any friendly ships in the area, is anyone there?"

"This is Admiral Hackett of Sword Fleet, we hear you loud and clear"

"Boy are we glad to hear from you Admiral. We thought we were on our own for awhile. It's not pretty down here, but all Reaper forces have been eradicated. It worked. Shepard did it."

"Yes, he certainly did. We are sending ships down to assist you. So begins the long road of recovery. Hackett out."

Hackett closed the comm.


	2. Chapter 1: Shepard

"Shepard."

Commander John Shepard hastily woke up as he heard a voice whisper his name. In a cold sweat, he looked around. Where was he? It looked like his quarters back on the Normandy SR-1, but that was impossible!

His mind raced back as far as he could remember. It all started coming back to him. The Citadel, Anderson, the Illusive Man, and the Catalyst AI that presented him his three choices. The last thing he could recall was angrily making the choice to annihilate the Reapers with the crucible. He just wanted them all gone after all the friends he lost, and between the other choices of becoming the Catalyst's replacement and rewriting every life form in the galaxy's DNA, it seemed like the soundest choice.

But where was he now? He reached for the door that led out to the Normandy's mess hall. "Locked." He groaned. "Go figure."

Suddenly, there was a high pitch ringing sound and he fell to the floor. It felt as if his mind was being split in two. Then he heard more voices.

"There's no time, get Alenko and get out of here Commander! You know it's the right choice!"

Ashley. The first friend he lost. He remembered how angry he was after her untimely death, and promised to never lose another crew member.

A promise he couldn't keep.

Another voice. Frantic and frightened.

"Mayday! Mayday! This is SSV Normandy! We have suffered massive damage from an unknown enemy!"

His mind immediately rushed back to the Collector attack on the SR-1. He remembered watching his crew die around him, rushing to the bridge trying to save Joker...

And then he died. What kind of Captain was he? He couldn't even guarantee the safety of himself, let alone his crew.

"Had to be me, someone else might have gotten it wrong."

Mordin chose to sacrifice himself, but Shepard still felt guilty about it. The Salarian scientist and former STG Member gave his life to save a species he originally condemned to extinction.

"There seems there will be no one to morn me when I die. You're the only friend I've made in years."

Thane. Shepard never knew an assassin could teach him so much about life. Thane's life was a tragedy, and he was dying already, but those damn Cerberus bastards had to be the ones to end him. He may have been an assassin, but he died a hero.

"You did good son. You did good. I'm...proud...of you."

Anderson. The one who had been at his side since the beginning. That one hit him the hardest.

There was another high pitch noise, and suddenly, he was lying besides Anderson on the Citadel, watching as the arms opened. He remembered seeing shield fleet getting ripped apart by Reapers as they struggled to get the crucible docked. It was a miracle that they docked, let alone survived.

The voices stopped, and Shepard wondered "What the hell is going on? Am I...in hell?"

Everything went white.

Shepard awoke finding himself strapped to an operating table. He couldn't feel anything, and he couldn't move. Was he reliving Project Lazarus now? He gazed around the room, expecting to find the orange and black symbols on the wall, but there were none. Instead, the blue insignia of the Systems Alliance decorated the room. His hearing started to come back, and he suddenly heard what was going on around him. A heartbeat monitor, beepings very fast. The hustle of doctors around the room. One of them yelled.

"Shepard is awake! Quick, administer the sedatives! The cellular regeneration is not complete! Shepard, if you can hear me, just relax."

He saw a syringe enter his arm, and then everything went black.

**Alright, that's chapter two. In the following chapters, we will get to see how Shepard was found and what became of the Normandy SR-2. Thanks for reading and please review!**


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